Is there anyone can share some tips or experience of using qRT-PCR to detect RNAi effects in plant? For example, which region should I design primer/probe? If I have a RNAi vector using full length cDNA for both sense and antisense, can I still detect the gene suppression with qRT-PCR?

Thanks for your reply. I am still not sure if I have found the right answer. First, I think siRNA and RNAi have different mechanism for knockdown mRNA. Second, is it possible that the primer/probe also binds to the sense and antisense region from vector? Is it possible that the qPCR detects the region from vector in addition to the gene from plant? Those questions have bothered me for a while but I haven't found any clear answer or good reference paper yet.